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- PDB-2p4z: A Ferredoxin-like Metallo-beta-lactamase Superfamily Protein from... -

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Basic information

Entry
Database: PDB / ID: 2p4z
TitleA Ferredoxin-like Metallo-beta-lactamase Superfamily Protein from Thermoanaerobacter tengcongensis
ComponentsMetal-dependent hydrolases of the beta-lactamase superfamily II
KeywordsHYDROLASE / Metal-dependent hydrolases of the beta-lactamase superfamily II
Function / homology
Function and homology information


transferase activity / hydrolase activity / metal ion binding
Similarity search - Function
Methanocaldococcus jannaschii dihydropteroate synthase-like, MBL-fold metallo hydrolase domain / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Metal-dependent hydrolases of the beta-lactamase superfamily II
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsLiang, D.-C. / Gu, S.-Y.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of Tflp: A ferredoxin-like metallo-beta-lactamase superfamily protein from Thermoanaerobacter tengcongensis
Authors: Gu, S.-Y. / Yan, X.-X. / Liang, D.-C.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-dependent hydrolases of the beta-lactamase superfamily II
B: Metal-dependent hydrolases of the beta-lactamase superfamily II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7536
Polymers64,5302
Non-polymers2234
Water3,567198
1
A: Metal-dependent hydrolases of the beta-lactamase superfamily II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3773
Polymers32,2651
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metal-dependent hydrolases of the beta-lactamase superfamily II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3773
Polymers32,2651
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870.9 Å2
ΔGint-70.6 kcal/mol
Surface area21596.8 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.197, 138.310, 52.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Metal-dependent hydrolases of the beta-lactamase superfamily II


Mass: 32264.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q8R8V2
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24.5% Pentaerythritol propoxylate (5/4 PO/OH), 0.1M Bis-Tris, 0.08M Ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 34056 / Num. obs: 34056 / Redundancy: 10 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.1→2.15 Å / Num. unique all: 34056

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.487 / SU ML: 0.121 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21855 1650 5.1 %RANDOM
Rwork0.20023 ---
obs0.20118 30853 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.691 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---1.88 Å20 Å2
3---3.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 4 198 4576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9585983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68524.683205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3891518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023280
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23041
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8951.52793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12124368
X-RAY DIFFRACTIONr_scbond_it1.78231851
X-RAY DIFFRACTIONr_scangle_it2.764.51615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 100 -
Rwork0.219 1632 -
obs--71.84 %

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